Sun Blade 6048 and Sun Blade X6275 NAMD Molecular Dynamics Benchmark beats IBM BlueGene/L
By Russell Brown on Nov 20, 2009
Significance of ResultsA Sun Blade 6048 chassis with 48 Sun Blade X6275 server modules ran benchmarks using the NAMD molecular dynamics applications software. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is driven by major trends in computing and structural biology and received a 2002 Gordon Bell Award.
The cluster of 32 Sun Blade X6275 server modules was 9.2x faster than
the 512 processor configuration of the IBM BlueGene/L.
The cluster of 48 Sun Blade X6275 server modules exhibited excellent
scalability for NAMD molecular
dynamics simulation, up to 37.8x speedup for 48 blades relative to 1 blade.
- For largest molecule considered, the cluster of 48 Sun Blade X6275 server modules achieved a throughput of 0.028 seconds per simulation step.
Performance LandscapeThe NAMD Performance Benchmarks web page plots the performance of NAMD when the ApoA1 benchmark is executed on a variety of clusters. The performance is expressed in terms of the time in seconds required to execute one step of the molecular dynamics simulation, multiplied by the number of "processors" on which NAMD executes in parallel. The following table compares the performance of the Sun Blade X6275 cluster to several of the clusters for which performance is reported on the web page. In this table, the performance is expressed in terms of the time in seconds required to execute one step of the molecular dynamics simulation. A smaller number implies better performance.
|Cluster Name and Interconnect||Throughput for 128 Cores
(seconds per step)
|Throughput for 256 Cores
(seconds per step)
|Throughput for 512 Cores
(seconds per step)
|Sun Blade X6275 InfiniBand||0.014||0.0073||0.0048|
|Cambridge Xeon/3.0 InfiniPath||0.016||0.0088||0.0056|
|NCSA Xeon/2.33 InfiniBand||0.019||0.010||0.008|
|AMD Opteron/2.2 InfiniPath||0.025||0.015||0.008|
|IBM HPCx PWR4/1.7 Federation||0.039||0.021||0.013|
|SDSC IBM BlueGene/L MPI||0.108||0.061||0.044|
The following tables report results for NAMD molecular dynamics using a cluster of Sun Blade X6275 server modules. The performance of the cluster is expressed in terms of the time in seconds that is required to execute one step of the molecular dynamics simulation. A smaller number implies better performance.
|Blades||Cores||STMV molecule (1)||f1 ATPase molecule (2)||ApoA1 molecule (3)|
spdup - speedup versus 1 blade result
effi'cy - speedup efficiency versus 1 blade result
(1) Satellite Tobacco Mosaic Virus (STMV) molecule, 1,066,628 atoms,
12 Angstrom cutoff, Langevin dynamics, 500 time steps
(2) f1 ATPase molecule, 327,506 atoms, 11 Angstrom cutoff, particle mesh Ewald dynamics, 500 time steps
(3) ApoA1 molecule, 92,224 atoms, 12 Angstrom cutoff, particle mesh Ewald dynamics, 500 time steps
Results and Configuration Summary
48 x Sun Blade X6275, each with
2 x (2 x 2.93 GHz Intel QC Xeon X5570 (Nehalem) processors)
2 x (24 GB memory)
Hyper-Threading (HT) off, Turbo Mode on
SUSE Linux Enterprise Server 10 SP2 kernel version 126.96.36.199-0.31_lustre.188.8.131.52-smp
gcc 4.1.2 (1/15/2007), gfortran 4.1.2 (1/15/2007)
Benchmark DescriptionMolecular dynamics simulation is widely used in biological and materials science research. NAMD is a public-domain molecular dynamics software application for which a variety of molecular input directories are available. Three of these directories define:
- the Satellite Tobacco Mosaic Virus (STMV) that comprises 1,066,628 atoms
- the f1 ATPase enzyme that comprises 327,506 atoms
- the ApoA1 enzyme that comprises 92,224 atoms
Key Points and Best Practices
Models with large numbers of atoms scale better than models with small numbers of atoms.
The Intel QC X5570 processors include a turbo boost feature coupled with a speed-step option in the CPU section of the Advanced BIOS settings. Under specific circumstances, this can provide cpu overclocking which increases the processor frequency from 2.93GHz to 3.33GHz. This feature was was enabled when generating the results reported here.